UC San Diego

Molecular dynamics (MD) simulation, an established method for investigating the internal motions of biomolecules, is applied to thrombin protein, a critical blood coagulation cascade protease with complex, not yet fully understood regulatory mechanisms. Accelerated MD (AMD) is employed to achieve enhanced conformational sampling of more biologically relevant timescales, and nuclear magnetic resonance (NMR) experiments are used to validate and tune AMD parameters. In chapter 1, the thrombin system and its interaction with cofactor thrombomodulin (TM) is introduced. The potential contribution of dynamics to thrombin allostery is discussed, and methods for MD and AMD simulations are described. In chapter 2, the combined use of NMR and AMD to examine the dynamics of thrombin is detailed. AMD generated ensembles are shown to recapitulate NMR residual dipolar couplings (RDCs), observables that report on ms timescale dynamics. The resulting picture of thrombin depicts a stable core surrounded by highly dynamic surface loops. In chapter 3, a computational study comparing isolated thrombin with TM bound forms is reported. Community network analysis identifies two allosteric pathways from the TM binding exosite to the thrombin active site. The presence of the fourth EGF-like domain of TM, known to be essential for thrombin regulation, is shown to establish and strengthen these allosteric pathways. This essential domain is also observed to elicit enhanced dynamics and cross-correlated motion in the distal active site loops. In chapter 4, these analyses are extended to compare apo thrombin with active site inhibitor bound thrombin. Allosteric pathways between the active and TM binding exosite site are again observed and are altered by the presence of inhibitor. Residual local frustration analysis reveals a minimally frustrated thrombin core surrounded by highly frustrated surface loops. The highly frustrated contacts regions show significant overlap with regions undergoing slow timescale dynamics. In chapter 5, overarching implications for a dynamical mechanism to thrombin:TM allostery are discussed. The collective observations of thrombin active site surface loops undergoing concerted, long timescale dynamics in response to TM binding at exosite 1 strongly suggest a dynamic, allosteric mechanism in thrombin regulation